Closed qdu-beep closed 5 months ago
oushujun
commented
5 months ago Hello,
If you are only interested in the LTRs, you should just run LTR_retriever. The EDTA_raw.pl --type ltr will get you there, but without whole-genome annotation. You can do your own by running RepeatMasker -lib $genome.mod.LTRlib.fa within EDTA.raw/LTR/. After RepeatMasking, you can run make_masked.pl for soft masking.
Shujun
qdu-beep
commented
5 months ago Hello,
If you are only interested in the LTRs, you should just run
LTR_retriever. TheEDTA_raw.pl --type ltrwill get you there, but without whole-genome annotation. You can do your own by runningRepeatMasker -lib $genome.mod.LTRlib.fawithinEDTA.raw/LTR/. After RepeatMasking, you can runmake_masked.plfor soft masking.Shujun
Dear oushujun,
Many thanks for your useful reply! My question has been resolved!
Sincerely, qdu-beep
I would like to ask if I want to obtain the genome sequence with only LTR regions masked and using soft-masking, should I follow the steps below? The main question is whether I should use EDTA.pl after using raw_EDTA.pl. I would greatly appreciate your response!
Should I use EDTA_raw.pl with the -type ltr to obtain the raw library of LTR? And then, should I use EDTA.pl with the --overwrite 0 to further annotate and filter based on the results of raw_EDTA.pl? Finally, I should use make_masked.pl for soft masking.
I came across the following description on the website, but I'm not sure if my understanding is correct. Thank you for your assistance! "Users may run EDTA_raw.pl for each TE type with --threads 1, then run EDTA.pl with multi threads and --overwrite 0"(https://github.com/oushujun/EDTA/releases) Originally posted by @qdu-beep in https://github.com/oushujun/EDTA/issues/61#issuecomment-1870767074